in reply to how to create output file using perl

welcome to the monastery vineetha,

more effort you put asking best chances you have to get back a good answer.
You assume (and you are wrong) that every monk will understand your post and the solution is clear for people knowing Perl.
If you think that me or other go on the web to learn what blast, contigs and sequences are just to compose a reply to your question, you are too much optimistic..

Anyway if you can produce some small example, or even better, if you can reduce your problem to something widely understandable, chances are that you'll receive good replies.

if you have some Perl knoweledge the basic structure of your program will be something like: 
##PSEUDOCODE
read from file A
read from file B
process data 
write output to file C

[download]


L*
There are no rules, there are no thumbs..
Reinvent the wheel, then learn The Wheel; may be one day you reinvent one of THE WHEELS.

Replies are listed 'Best First'.
Re^2: BLAST RESULT FILE
by vineetha (Initiate) on Jul 01, 2015 at 09:53 UTC 
    BLAST RESULT FILE

BLASTN 2.2.31+


Reference: Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb
Miller (2000), "A greedy algorithm for aligning DNA sequences", J
Comput Biol 2000; 7(1-2):203-14.

 

Database: Arabidopsis_thaliana.mRNA.EST.fasta
           1,529,700 sequences; 400,627,814 total letters

 

Query= Contig1

Length=941
                                                                      
+Score     E
Sequences producing significant alignments:                          (
+Bits)  Value

  gi|61656031|gb|DN604734.1|DN604734 EST JCAt1g22640 Arabidopsis ...  
+219     4e-055
 

> gi|61656031|gb|DN604734.1|DN604734 EST JCAt1g22640 Arabidopsis 
Gateway cDNA Library Arabidopsis thaliana cDNA 3', mRNA sequence.
Length=740

 Score = 219 bits (118),  Expect = 4e-055
 Identities = 263/334 (79%), Gaps = 6/334 (2%)
 Strand=Plus/Minus

Query  60   AAAGGAGCTTGGACTAAAGAAGAAGATGAACGACTTATTTCTTATAT--TAAAACTCA
+CG  117
            ||||||||||||||||||||||||||| | |  ||| ||  ||| ||    |||  ||
+||
Sbjct  734  AAAGGAGCTTGGACTAAAGAAGAAGATCAGCTTCTTGTTGATTACATCCGTAAA--CA
+CG  677

Query  118  GCGAAGGTTGCTGGAGATCCCTTCCTAAAGCTGCCGGACTTCTCCGATGCGGTAAAAG
+TT  177
            | |||||||||||| |||| || |||   || || ||| | |   |||| ||||| ||
+||
Sbjct  676  GTGAAGGTTGCTGGCGATCTCTCCCTCGCGCCGCTGGATTACAAAGATGTGGTAAGAG
+TT  617

Query  178  GCCGTCTCCGATGGATTAATTACTTGAGACCGGACCTTAAACGCGGTAATTTTACTGA
+AG  237
            |  |  |  ||||||| |||||  | ||||| || || ||| | || |||||||||||
+||
Sbjct  616  GTAGATTGAGATGGATGAATTATCTAAGACCAGATCTCAAAAGAGGCAATTTTACTGA
+AG  557

Query  238  AAGAAGATGAACTCATTATCAAACTCCATAGCCTCCTTGGTAACAAATGGTCACTTAT
+AG  297
            |||||||||||||||| ||||| ||||||||| | || ||||||||||||||  | ||
+||
Sbjct  556  AAGAAGATGAACTCATCATCAAGCTCCATAGCTTGCTCGGTAACAAATGGTCTTTAAT
+AG  497

Query  298  CCGGAAGATTACCAGGAAGAACAGATAATGAGATAAAAAATTACTGGAATACGCACAT
+-A  356
            | || ||||||||||||||||||||||| ||||| || || || ||||| || || ||
+ |
Sbjct  496  CTGGGAGATTACCAGGAAGAACAGATAACGAGATCAAGAACTATTGGAACACTCATAT
+CA  437

Query  357  AGAAGGAAGCTTTTGAGTCGGGGCATTGATCCAA  390
            || ||||||||| | || || || ||||||||||
Sbjct  436  AG-AGGAAGCTTCTCAGCCGTGGGATTGATCCAA  404

Lambda      K        H
    1.33    0.621     1.12 

Gapped
Lambda      K        H
    1.28    0.460    0.850 

Effective search space used: 326667943382


Query= Contig2

Length=1009


***** No hits found *****

 

Lambda      K        H
    1.33    0.621     1.12 

Gapped
Lambda      K        H
    1.28    0.460    0.850 

Effective search space used: 350998085934


Query= Contig3

Length=529


***** No hits found *****

 

Lambda      K        H
    1.33    0.621     1.12 

Gapped
Lambda      K        H
    1.28    0.460    0.850 

Effective search space used: 180381608828


Query= Contig4

Length=896
                                                                      
+Score     E
Sequences producing significant alignments:                          (
+Bits)  Value

  gi|152034016|gb|AU239642.2|AU239642 EST AU239642 RAFL21 Arabido...  
+167     1e-039

> gi|152034016|gb|AU239642.2|AU239642 EST AU239642 RAFL21 Arabidopsis 
thaliana cDNA clone RAFL21-11-C04 5', mRNA sequence.
Length=632

 Score = 167 bits (90),  Expect = 1e-039
 Identities = 260/345 (75%), Gaps = 2/345 (1%)
 Strand=Plus/Plus

Query  232  ATTGCCAATACTAAGTCTTGGTTCCAATTCTATGGCGACGGCTTTTCTATTCGTGTTC
+CA  291
            ||||| || ||||||||||||||||| | || |||    || ||  ||||| | ||||
+| 
Sbjct  286  ATTGCGAACACTAAGTCTTGGTTCCAGTACTTTGGTAGTGGGTTCGCTATTAGGGTTC
+CT  345

Query  292  CCGGAATTTCAGGACCTCACTGAGCCGGAGGATTATAATGCTGGCCTATCACTATATG
+GA  351
            || || ||| | ||| ||| |||||| ||||||||   ||| ||  | || || ||||
+| 
Sbjct  346  CCTGACTTTGAAGACGTCAATGAGCCTGAGGATTACTCTGCGGGATTGTCTCTCTATG
+GT  405

Query  352  GATAAGGCTAAGCCCAAAAAATTT-GCAGCACGTTTTGCTTCTTCTGATGGATCCGAA
+GT  410
            || ||||| ||||| | ||| ||| || || || ||     || |||||||||| |||
+||
Sbjct  406  GACAAGGCAAAGCC-ACAAACTTTCGCCGCCCGGTTCCAAACTCCTGATGGATCAGAA
+GT  464

Query  411  TTTAAGTGTCATAATTCGTCCATCCAATCAGCTGAAGATCACTTTCTTAGAGGCTAAA
+GA  470
            ||| |||||  | |||||||| || ||||| || ||||||||||||||||||||||||
+||
Sbjct  465  TTTGAGTGTAGTCATTCGTCCTTCAAATCAACTTAAGATCACTTTCTTAGAGGCTAAA
+GA  524

Query  471  TATTACTGATTTAGGTTCACTTAAGGAGGCAGCAAAAATATTTGTTCCAGCTGGCTCA
+AC  530
            |||  ||||||| || ||| | ||||  || |||| | | |||||||||| ||   ||
+||
Sbjct  525  TATATCTGATTTGGGATCATTGAAGGCAGCTGCAAGACTTTTTGTTCCAGGTGCNGCA
+AC  584

Query  531  ACTATATTCTGTCCGCACAATAAAAATTAAAGAAGATGAGGGTTT  575
            | | || ||||  || ||||| ||  | || ||||| || |||||
Sbjct  585  AATTTACTCTGCTCGTACAATCAAGGTAAAGGAAGAAGAAGGTTT  629

Lambda      K        H
    1.33    0.621     1.12 

Gapped
Lambda      K        H
    1.28    0.460    0.850 

Effective search space used: 310567113752

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[d/l]
Re^2: CONTIG FILE
by vineetha (Initiate) on Jul 01, 2015 at 09:57 UTC 
    CONTIG FILE

>Contig1
GAGCTAAATAATTTGAATCAATGGGAAGATCACCGTGTTGTGAAAAAGCACATACAAATAAAGGAGCTTG
+GACTAAAGAAGAAGATGAACGACTTATTTCTTATATTAAAACTCACGGCGAAGGTTGCTGGAGATCCCT
+TCCTAAAGCTGCCGGACTTCTCCGATGCGGTAAAAGTTGCCGTCTCCGATGGATTAATTACTTGAGACC
+GGACCTTAAACGCGGTAATTTTACTGAAGAAGAAGATGAACTCATTATCAAACTCCATAGCCTCCTTGG
+TAACAAATGGTCACTTATAGCCGGAAGATTACCAGGAAGAACAGATAATGAGATAAAAAATTACTGGAA
+TACGCACATAAGAAGGAAGCTTTTGAGTCGGGGCATTGATCCAACGACACACAGGCCTGTTAACGAGCC
+TGGTACAACGCAAAAAGTCACAACAATTTCATTTGCAGGTGGAGATCATAAAACTAAAGATATTGAAGA
+AGATCATAATAAGATGATAAATGTCAAAGCTGAATCTGGGTTGAGTCAATTAGAAGATGAAATTATTAG
+TAGCAGTCCATTTCGAGAACAGTGTCCTGATTTAAATCTTGAGCTCAAATTAGCCCTCCTTCTCTACAA
+AATTACCAACATAGCCCCTCAAGGTGTTTTGCATGCAGTTTGGGTATACAAAATAGTAAAGATTGCAAT
+TGCAGTAAAAATAATATTGCAAGTTATAACTTTTTAGGATTAAAGAGTAATGGTGTTTTGGACTATAGA
+ACTTTAGAAACTAAGTGAATTTTTATTATAAATCTTTTTTTCCCTCGTGTATTTGGGTTAAAAAAACAA
+GAAGAGAGAATCGAGAAAGATATTCCTATTAGTTTAAGTTCTTTCGAATTTTCTCTTATTTGTAAAATT
+TCAAGTATTACTATATACGATATATTATATTAAGTTGAAAAG
>Contig2
GCTCTTCCAACAACAACAACAATGCCTCATCAAAAGCCTCTTTCTCTCATTCTTCTATCTACACTCCCAC
+TTCTTTTCATTCTCACACAAGCTCAATCACCAACAGCACCAGCACCAGCACCCTCAGGACCAATAGACA
+TCTTTGCAATCCTCAAAAAAGAAGGACAATACAACACATTCATCAAGTTCCTAAATGAATCACAAGTTG
+GTAACCAAATCAACAACCAAGTAAACAACTCCAACCAAGGCATGACAGTTTTGGCACCATCAGACAATG
+CATTTAACAACCTCCCAAGTGGTACACTCAACCAACTAAATGACCAACAAAAAGTACAACTCATTTTGA
+ACCATGTCATACCAAAGTTCTACACATTTGATGACTTACAAACAGTAAGCAACCCTGTTAGAACACAAG
+CAACAGGGCCTAAAGGTGAGCCTTTTGGACTTAACTTTACTGGAAGTAACAATCAAGTGAATGTCTCAT
+CTGGTTCTGTTGTTACAAACATTTATAATGCTATTAGAAAAGACCCCCCATTGGCTGTTTTTCAATTAG
+ACAAAGTTTTAGTACCTTCTCAGTTTACTGATCCATCTAGTGATGATGATGCCCCTGCACCTACTAAAC
+CCAAGAATGGTACTAGTAATGATAAAACAACAGCTGATGAGCCATCACCAGCAAGTAACACTAAGCCAA
+ATGATGCTAAAAGGATCAGTGGTGGGATTCTTGGATTGGTTTGTGGTGTTTTCTTGATGGCAACACTAT
+CTTGAAGGGGGCTACAGAGTTGTTAACTTTATGATCTTTTGCTTATACTAAGCCATTTTGTATTACATT
+GTTTTCTTCAAGATTGATTGTTTTTGTTCAAAAAAGAAGGGGGGGGGGGAAAAAAAAACCCCCCTGCGG
+AAAAGAGCGGGGAAAGCACCAAAAAGCCACCGACCAAAAGCACCAACTCACAAAAGGTGCGCAGACGCG
+GAAAGGGGAAAAGGAAAAAATGTGAAAGCTTGTTATAGTTTG
>Contig3
AAACTGTAATTAGACTTCTCTGCTAAGTTTCTGCTGTATTTGGATTCTCCGGCGAACATTAATATCTAAC
+CATGACCGGCGGTGGAGGCGATGCCGCATCGCCGCCTCTATCCTCACAGTCAACTCCATCCAACGGTGG
+GGAATTCCTTCTTCAATTGCTTCAGAATCATCCGCATCAACTTCACTCTCAGCCTCAACCGCCACTGCG
+GCCGGAGTTGCAGAATCTGCCGCATGATCCAGCAGTTGCAGCAGTAGGTCCTAGTATGCCCTACCCGCC
+ATTGTTCCATACTCCTACAAACCCTTCTGTTTTGCCCTATTCTCACTCTCCTCCTCTGTTTGTACCTCA
+TAACTTCTTCATTCGAGGGTTTCTCCAAAACCCTAATTCTGGCCATACCACTAACCCCAATTACTCATC
+TCCGCCTGCCCCAAGTGGGTTCAGTCAATATCACCATGCGAGTCCACTTGGATTTGGATCAGTCGGAGA
+AAACATGGGCAATTTGGGGATTTTCGGTGCCAATGCTAAGGCGAG
>Contig4
CATGTAATAGCATAGCATCCCCAATTTCACCCTCTCATGGCCATGTCCACGCTCCTCTCCCTGTCCGTGT
+CTATCCACCCACCAAAACCTTTGCAAAAACCCAATTCAATGTGTACCCAACCTAACTCTATTTCGAGAA
+GACAAGTGTTTTTCACTGGTTCTAATTTATTGCTCTCTCAATTAATTCCAAAATCCGACGCCCAAACCA
+ATTCCAATAGTTTTCTTTCAGGTATTGCCAATACTAAGTCTTGGTTCCAATTCTATGGCGACGGCTTTT
+CTATTCGTGTTCCACCGGAATTTCAGGACCTCACTGAGCCGGAGGATTATAATGCTGGCCTATCACTAT
+ATGGAGATAAGGCTAAGCCCAAAAAATTTGCAGCACGTTTTGCTTCTTCTGATGGATCCGAAGTTTTAA
+GTGTCATAATTCGTCCATCCAATCAGCTGAAGATCACTTTCTTAGAGGCTAAAGATATTACTGATTTAG
+GTTCACTTAAGGAGGCAGCAAAAATATTTGTTCCAGCTGGCTCAACACTATATTCTGTCCGCACAATAA
+AAATTAAAGAAGATGAGGGTTTCAGGACATACTATTTTTATGAATTTGTGAGAAATGAGCAACACGTTG
+CATTAGTGGCTGGTGTTAACAGTGGAAAGGCCGTCATTGCTGGTGCCACGGCCCCCGAAAGCAAATGGG
+CCGAGGATGGTTTGAAGCTCCGATCTGCTGCAGTATCAATGACAATTCTATAAGCAGAATGTGAGTATA
+TATATAGGTTCTATTTCAATGATGATGAATTTATATACAAATATTGAGGATCAAAGTTTTCTTATTATC
+ATCTAATCTCAGCCAAGGATTAACAATCTCCATCATCCATTCAATAGCAATGTTTCTGCTGTTTTGC

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[d/l]
Re^2: how to create output file using perl
by vineetha (Initiate) on Jul 01, 2015 at 09:59 UTC
    These are the two files.In the blast result contig2 and contig 3 shows no blast hits so i need to extract these 2 contig sequences from contig file and print into a seperate text file
[reply]

      When you post it clearly says:

      Use:  <p> text here (a paragraph) </p>
      and:  <code> code here </code>
      to format your post; it's "PerlMonks-approved HTML":

      Please do so. Take the time to read and understand How do I post a question effectively?. What part of this task are you having problems with? Show us your code and the output.

[reply]

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