variables - How to modify a python script to call an external file during a batch process? -


i have long series of files need analyze, in batch, using python script, e.g.,:

all_transcriptomes.fasta ofas000003-ra_rbh.fasta ofas000101-ra_rbh.fasta ofas000115-ra_rbh.fasta ofas000119-ra_rbh.fasta

and on. need query each *rbh.fasta against all_transcriptomes.fasta.

here beginning section of script i'm using perform analysis (up specifying variables):

#!/usr/bin/env python usage = """this program entire reciprocal blast search. nomenclature follows: sequences vs sequences b blast search step 1 = seqs vs blast database of seqs b step 2 (this step) = seqs b vs blast database of seqs  columns of results table must follows:  column 1: query id column 2: query length column 3: subject id column 4: subject length column 5: bitscore column 6: e-value column 7 onwards can like.   """  #import modules needed import subprocess  #give information required print "\na program run full reciprocal blast program. \n\ if having problems, worth reading usage assumptions , lay out\n\n"  #the inputs required follows:\n\n\ #\ #1. project name\n\n\ #\ #2. name of fasta files containing first [a] set of sequences (must in working folder)\n\n\ #\ #3. name of fasta files containing second [b] set of sequences (must in working folder)\n\n\ #\ #4. kind of blast search doing?\n\n\ #\ #5. e-value cut-off like?\n\n\"  #get required inputs projectname = "project_name"  seqsfastaa = "query_file_name.fasta" #seqsfastaa = "temp_seqs.fasta"  seqsfastab = "all_transcriptomes.fasta" #seqsfastab = "temp_seqs.fasta"  blasttype = "blastn" #blasttype = "blastn"  evalue = "1e-20" #evalue = 1e-05

because of lack of python scripting experience, not know how can script call each ofas*.fasta seqsfastaa. projectname same ofas*.fasta file names, without .fasta. can assist modifying script when called batch shell script?


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