how to create an output file using perl

vineetha · 06-30-2015, 01:34 AM

I have two files.One file contains blast result of contigs and the next file contains the contigs that are used for blast.I want an output text file of sequences in a separate folder which gives no hits in blast result from original fasta file with all contigs.I have no idea about this.Can you please help me to create perl script for this problem.

Help me pleaseee...

wyzandrea · 06-30-2015, 02:25 AM

I want to ask this question too.

swbarnes2 · 07-01-2015, 12:06 PM

I don't think anyone wants to write a blast parser for you. If you are using blast from the command line, you can tell it to format the output a number of ways, one of those ways might be easier to parse for what you want.

SNPsaurus · 07-01-2015, 03:51 PM

If you want an output file with the "no hits", you could just grep the blast file for "no hits", with -B to grab the query, then grep that to get all the querys only, then grep the blast file with the query file using -f and with grep -A to get the sequence itself. Need to convert the fasta file to single line fasta, though.

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07-01-2015, 03:51 PM	#4
SNPsaurus Registered Vendor Location: Eugene, OR Join Date: May 2013 Posts: 521	If you want an output file with the "no hits", you could just grep the blast file for "no hits", with -B to grab the query, then grep that to get all the querys only, then grep the blast file with the query file using -f and with grep -A to get the sequence itself. Need to convert the fasta file to single line fasta, though. __________________ Providing nextRAD genotyping and PacBio sequencing services. http://snpsaurus.com

06-30-2015, 02:25 AM	#2
wyzandrea Banned Location: USA Join Date: Apr 2015 Posts: 2	I want to ask this question too.

07-01-2015, 12:06 PM	#3
swbarnes2 Senior Member Location: San Diego Join Date: May 2008 Posts: 912	I don't think anyone wants to write a blast parser for you. If you are using blast from the command line, you can tell it to format the output a number of ways, one of those ways might be easier to parse for what you want.