combine python function with for loops in bash terminal

Question

I aimed to open multiple files (one by one, using for loop in bash terminal) and modify it using PLINK (a programme) and later on, python function. Following are the codes:

for i in {1..10}; do
  plink --cow --noweb --lfile $i --extract extract1.snp --recode --out 1$i
  python -c 'import file_convert;file_convert.convert_tree_mix("1$i.map","tmp$i")'
done

But, as expected, python could not read and could not open "11.map", it did not replace "$i" with 1. How can i modify the code so that python function, in combination with for loop, open different file each time based on the value of "i"

try python -c "import file_convert;file_convert.convert_tree_mix(\"1$i.map\",\"tmp$i\")" — Avinash Raj
– Avinash Raj, Commented May 29, 2015 at 13:47

alagner · Accepted Answer · 2015-05-29 13:50:37Z

3

Have you tried calling python like that:

python -c 'import sys; import file_convert;file_convert.convert_tree_mix(sys.argv[1],sys.argv[2])' "1$i.map" "tmp$i";

?

answered May 29, 2015 at 13:50

alagner

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1 Comment

chepner Over a year ago

In general, this is better than trying to use shell interpolation to build a dynamic string for Python to execute.

Avinash Raj · Accepted Answer · 2015-05-29 14:07:54Z

0

You need to include the whole python code inside double quotes, so that the $1 inside the python code will expand. $1 in shell refers to the first parameter.

python -c "import file_convert;file_convert.convert_tree_mix(\"1$i.map\",\"tmp$i\")"

answered May 29, 2015 at 14:07

Avinash Raj

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